NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | position | program | type |
|
|
511707 |
2l94   |
17436 | cing | 1-original | 2 | XPLOR/CNS | planarity |
{=========================================================================================================}
{ things below this line do not normally need to be changed - but they have been by rjm }
{=========================================================================================================}
) {- end block parameter definition -}
{- planarity restraints for DB213 -}
{*
evaluate ($plweight = 20) !weighting for DB213 planarity
restraints plane
group
selection=((resid 1 and name N21 and segid B) or (resid 1 and name C11 and segid B) or
(resid 1 and name N111 and segid B) or (resid 1 and name C1 and segid B) or
(resid 1 and name C2 and segid B) or (resid 1 and name C6 and segid B))
weight=$plweight
end
group
selection=((resid 1 and name N24 and segid B) or (resid 1 and name C14 and segid B) or
(resid 1 and name N114 and segid B) or (resid 1 and name C4 and segid B) or
(resid 1 and name C5 and segid B) or (resid 1 and name C3 and segid B))
weight=$plweight
end
end
*}
{- the planarity restraints for Watson-Crick base pairing -}
if (&basepair_planar=true) then
evaluate ($plweight = 100) !Default = 20, enforce planarity by increasing plweight value.
restraints plane
group
selection=((resid 1 and name N1 and segid A) or (resid 1 and name N3 and segid A) or
(resid 1 and name C5 and segid A) or (resid 45 and name N1 and segid A) or
(resid 45 and name N3 and segid A) or (resid 45 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 2 and name N1 and segid A) or (resid 2 and name N3 and segid A) or
(resid 2 and name C5 and segid A) or (resid 44 and name N1 and segid A) or
(resid 44 and name N3 and segid A) or (resid 44 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 3 and name N1 and segid A) or (resid 3 and name N3 and segid A) or
(resid 3 and name C5 and segid A) or (resid 43 and name N1 and segid A) or
(resid 43 and name N3 and segid A) or (resid 43 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 4 and name N1 and segid A) or (resid 4 and name N3 and segid A) or
(resid 4 and name C5 and segid A) or (resid 42 and name N1 and segid A) or
(resid 42 and name N3 and segid A) or (resid 42 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 5 and name N1 and segid A) or (resid 5 and name N3 and segid A) or
(resid 5 and name C5 and segid A) or (resid 41 and name N1 and segid A) or
(resid 41 and name N3 and segid A) or (resid 41 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 6 and name N1 and segid A) or (resid 6 and name N3 and segid A) or
(resid 6 and name C5 and segid A) or (resid 40 and name N1 and segid A) or
(resid 40 and name N3 and segid A) or (resid 40 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 7 and name N1 and segid A) or (resid 7 and name N3 and segid A) or
(resid 7 and name C5 and segid A) or (resid 39 and name N1 and segid A) or
(resid 39 and name N3 and segid A) or (resid 39 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 9 and name N1 and segid A) or (resid 9 and name N3 and segid A) or
(resid 9 and name C5 and segid A) or (resid 34 and name N1 and segid A) or
(resid 34 and name N3 and segid A) or (resid 34 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 10 and name N1 and segid A) or (resid 10 and name N3 and segid A) or
(resid 10 and name C5 and segid A) or (resid 33 and name N1 and segid A) or
(resid 33 and name N3 and segid A) or (resid 33 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 11 and name N1 and segid A) or (resid 11 and name N3 and segid A) or
(resid 11 and name C5 and segid A) or (resid 32 and name N1 and segid A) or
(resid 32 and name N3 and segid A) or (resid 32 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 12 and name N1 and segid A) or (resid 12 and name N3 and segid A) or
(resid 12 and name C5 and segid A) or (resid 31 and name N1 and segid A) or
(resid 31 and name N3 and segid A) or (resid 31 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 13 and name N1 and segid A) or (resid 13 and name N3 and segid A) or
(resid 13 and name C5 and segid A) or (resid 30 and name N1 and segid A) or
(resid 30 and name N3 and segid A) or (resid 30 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 14 and name N1 and segid A) or (resid 14 and name N3 and segid A) or
(resid 14 and name C5 and segid A) or (resid 29 and name N1 and segid A) or
(resid 29 and name N3 and segid A) or (resid 29 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 15 and name N1 and segid A) or (resid 15 and name N3 and segid A) or
(resid 15 and name C5 and segid A) or (resid 28 and name N1 and segid A) or
(resid 28 and name N3 and segid A) or (resid 28 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 16 and name N1 and segid A) or (resid 16 and name N3 and segid A) or
(resid 16 and name C5 and segid A) or (resid 27 and name N1 and segid A) or
(resid 27 and name N3 and segid A) or (resid 27 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 17 and name N1 and segid A) or (resid 17 and name N3 and segid A) or
(resid 17 and name C5 and segid A) or (resid 26 and name N1 and segid A) or
(resid 26 and name N3 and segid A) or (resid 26 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 18 and name N1 and segid A) or (resid 18 and name N3 and segid A) or
(resid 18 and name C5 and segid A) or (resid 25 and name N1 and segid A) or
(resid 25 and name N3 and segid A) or (resid 25 and name C5 and segid A))
weight=$plweight
end
group
selection=((resid 19 and name N1 and segid A) or (resid 19 and name N3 and segid A) or
(resid 19 and name C5 and segid A) or (resid 24 and name N1 and segid A) or
(resid 24 and name N3 and segid A) or (resid 24 and name C5 and segid A))
weight=$plweight
end
{*
group
selection=((resid 20 and name N1 and segid A) or (resid 20 and name N3 and segid A) or
(resid 20 and name C5 and segid A) or (resid 23 and name N1 and segid A) or
(resid 23 and name N3 and segid A) or (resid 23 and name C5 and segid A))
weight=$plweight
end
*}
end
end if
flag include plan end
{- the planarity restraints single bases -}
for $id in id ( &bases_planar and tag ) loop plan
show (segid) (id $id)
evaluate ($segid=$result)
show (resid) (id $id)
evaluate ($resid=decode($result))
evaluate ($plweight = 20)
restraints plane
group
selection=( segid $segid and resid $resid and
(resname THY or resname CYT or resname GUA or
resname ADE or resname URI) and
not (name c#' or name h#' or name h#'' or name o#p or
name h7# or name o#' or name p or name h#t or name o#t))
weight=$plweight
end
end
end loop plan
flag include plan end
{- Dihedral restraints for the sugar pucker -}
if (&dna_pick_pucdih=true) then
evaluate ($group=1)
evaluate ($done=false)
while ( $done = false ) loop dihe
if ( &exist_pucker_$group = true ) then
show sum(1) ( &pucker_$group )
if ( $result > 0 ) then
evaluate ($min_resid_$group = 99999)
evaluate ($max_resid_$group = -99999)
evaluate ($error_nu2=&error_nu2_$group)
evaluate ($error_nu3=&error_nu3_$group)
evaluate ($error_nu4=&error_nu4_$group)
for $id in id ( &pucker_$group and tag ) loop resid
show (segid) (id $id)
evaluate ($segid=$result)
show (resid) ( id $id )
evaluate ($resid=decode($result))
evaluate ($min_resid_$group = max($min_resid_$group,$resid))
evaluate ($max_resid_$group = max($max_resid_$group,$resid))
pick dihedral
( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name c2' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c4' )
geometry
evaluatate ($dihedral_nu2=$result)
pick dihedral
( segid $segid and resid $resid and name c5' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c2' )
geometry
evaluatate ($dihedral_nu3=$result)
pick dihedral
( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name o4' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c5' )
geometry
evaluatate ($dihedral_nu4=$result)
restraints dihedral
assign ( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name c2' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c4' )
20.0 $dihedral_nu2 $error_nu2 2
assign ( segid $segid and resid $resid and name c5' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c2' )
20.0 $dihedral_nu3 $error_nu3 2
assign ( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name o4' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c5' )
20.0 $dihedral_nu4 $error_nu4 2
scale=20.0
end
end loop resid
end if
else
evaluate ($done=true)
end if
evaluate ($group=$group+1)
end loop dihe
else
evaluate ($group=1)
evaluate ($done=false)
while ( $done = false ) loop dihe
if ( &exist_pucker_$group = true ) then
show sum(1) ( &pucker_$group )
if ( $result > 0 ) then
if ( &form_$group = "a-form" ) then
evaluate ($dihedral_nu2=37.053)
evaluate ($dihedral_nu3=-155.59)
evaluate ($dihedral_nu4=144.26)
elseif ( &form_$group = "b-form" ) then
evaluate ($dihedral_nu2=-34.9)
evaluate ($dihedral_nu3=-86.4)
evaluate ($dihedral_nu4=106.4)
elseif ( &form_$group = "other" ) then
evaluate ($dihedral_nu2=&dihedral_nu2_$group)
evaluate ($dihedral_nu3=&dihedral_nu3_$group)
evaluate ($dihedral_nu4=&dihedral_nu4_$group)
end if
evaluate ($min_resid_$group = 99999)
evaluate ($max_resid_$group = -99999)
for $id in id ( &pucker_$group and tag ) loop resid
show (segid) (id $id)
evaluate ($segid=$result)
show (resid) ( id $id )
evaluate ($resid=decode($result))
evaluate ($min_resid_$group = max($min_resid_$group,$resid))
evaluate ($max_resid_$group = max($max_resid_$group,$resid))
restraints dihedral
assign ( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name c2' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c4' )
20.0 $dihedral_nu2 0.0 2
assign ( segid $segid and resid $resid and name c5' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c3' )
( segid $segid and resid $resid and name c2' )
20.0 $dihedral_nu3 0.0 2
assign ( segid $segid and resid $resid and name c1' )
( segid $segid and resid $resid and name o4' )
( segid $segid and resid $resid and name c4' )
( segid $segid and resid $resid and name c5' )
20.0 $dihedral_nu4 0.0 2
scale=20.0
end
end loop resid
end if
else
evaluate ($done=true)
end if
evaluate ($group=$group+1)
end loop dihe
end if
flags include cdih end
{- Dihedral restraints for the phosphate backbone -}
if (&dna_pick_bacdih=true) then
evaluate ($group=1)
evaluate ($done=false)
while ( $done = false ) loop bdihe
if ( &exist_dihedral_$group = true ) then
show sum(1) ( &dihedral_$group )
if ( $result > 0 ) then
evaluate ($resid=$min_resid_$group)
evaluate ($nres=$max_resid_$group - $min_resid_$group + 1)
evaluate ($error_alpha=&error_alpha_$group)
evaluate ($error_beta=&error_beta_$group)
evaluate ($error_gamma=&error_gamma_$group)
evaluate ($error_zeta=&error_zeta_$group)
evaluate ($error_epsilon=&error_eps_$group)
evaluate ($error_delta=&error_delta_$group)
for $id in id ( &dihedral_$group and tag ) loop resid
show (segid) (id $id)
evaluate ($segid=$result)
show (resid) ( id $id )
evaluate ($resid=decode($result))
if ($resid > $min_resid_$group) then
evaluate ($rprec = $resid - 1)
pick dihedral
( segid $segid and resid $rprec and name O3' )
( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
geometry
evaluatate ($dihedral_alpha=$result)
pick dihedral
( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
geometry
evaluatate ($dihedral_beta=$result)
restraint dihedral
! alpha
assign ( segid $segid and resid $rprec and name O3' )
( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
1.0 $dihedral_alpha $error_alpha 2
! beta
assign ( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
1.0 $dihedral_beta $error_beta 2
scale 200.0
end
end if
pick dihedral
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
geometry
evaluatate ($dihedral_gamma=$result)
pick dihedral
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
geometry
evaluatate ($dihedral_delta=$result)
restraints dihedral
! gamma
assign ( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
1.0 $dihedral_gamma $error_gamma 2
! delta
assign ( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
1.0 $dihedral_delta $error_delta 2
scale=200.0
end
if ($resid < $max_resid_$group) then
evaluate ($rfoll = $resid + 1)
pick dihedral
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
geometry
evaluatate ($dihedral_epsilon=$result)
pick dihedral
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
( segid $segid and resid $rfoll and name O5' )
geometry
evaluatate ($dihedral_zeta=$result)
restraint dihedral
! epsilon
assign ( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
1.0 $dihedral_epsilon $error_epsilon 2
! zeta
assign ( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
( segid $segid and resid $rfoll and name O5' )
1.0 $dihedral_zeta $error_zeta 2
scale 200.0
end
end if
end loop resid
end if
else
evaluate ($done=true)
end if
evaluate ($group=$group+1)
end loop bdihe
else
evaluate ($group=1)
evaluate ($done=false)
while ( $done = false ) loop bdihe
if ( &exist_dihedral_$group = true ) then
show sum(1) ( &dihedral_$group )
if ( $result > 0 ) then
evaluate ($resid=$min_resid_$group)
evaluate ($nres=$max_resid_$group - $min_resid_$group + 1)
if ( &form_$group = "a-form" ) then
evaluate ($dihedral_alpha=-70)
evaluate ($error_alpha=50)
evaluate ($dihedral_beta=180)
evaluate ($error_beta=50)
evaluate ($dihedral_gamma=60)
evaluate ($error_gamma=35)
evaluate ($dihedral_delta=81)
evaluate ($error_delta=20)
evaluate ($dihedral_zeta=-85)
evaluate ($error_zeta=50)
evaluate ($dihedral_epsilon=180)
evaluate ($error_epsilon=35)
elseif ( &form_$group = "b-form" ) then
evaluate ($dihedral_alpha=-63.6)
evaluate ($error_alpha=6)
evaluate ($dihedral_beta=176)
evaluate ($error_beta=7)
evaluate ($dihedral_gamma=51.4)
evaluate ($error_gamma=7)
evaluate ($dihedral_delta=128)
evaluate ($error_delta=13s)
evaluate ($dihedral_epsilon=-171.7)
evaluate ($error_epsilon=3.7)
evaluate ($dihedral_zeta=-103.8)
evaluate ($error_zeta=10)
elseif ( &form_$group = "other" ) then
evaluate ($dihedral_alpha=&dihedral_alpha_$group)
evaluate ($error_alpha=&error_alpha_$group)
evaluate ($dihedral_beta=&dihedral_beta_$group)
evaluate ($error_beta=&error_beta_$group)
evaluate ($dihedral_gamma=&dihedral_gamma_$group)
evaluate ($error_gamma=&error_gamma_$group)
evaluate ($dihedral_delta=&dihedral_delta_$group)
evaluate ($error_delta=&error_delta_$group)
evaluate ($dihedral_zeta=&dihedral_zeta_$group)
evaluate ($error_zeta=&error_zeta_$group)
evaluate ($dihedral_epsilon=&dihedral_eps_$group)
evaluate ($error_epsilon=&error_eps_$group)
end if
for $id in id ( &dihedral_$group and tag ) loop resid
show (segid) (id $id)
evaluate ($segid=$result)
show (resid) ( id $id )
evaluate ($resid=decode($result))
if ($resid > $min_resid_$group) then
evaluate ($rprec = $resid - 1)
restraint dihedral
! alpha
assign ( segid $segid and resid $rprec and name O3' )
( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
1.0 $dihedral_alpha $error_alpha 2
! beta
assign ( segid $segid and resid $resid and name P )
( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
1.0 $dihedral_beta $error_beta 2
scale 200.0
end
end if
restraints dihedral
! gamma
assign ( segid $segid and resid $resid and name O5' )
( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
1.0 $dihedral_gamma $error_gamma 2
!delta
assign ( segid $segid and resid $resid and name C5' )
( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
1.0 $dihedral_delta $error_delta 2
scale=200.0
end
if ($resid < $max_resid_$group) then
evaluate ($rfoll = $resid + 1)
restraint dihedral
! epsilon
assign ( segid $segid and resid $resid and name C4' )
( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
1.0 $dihedral_epsilon $error_epsilon 2
! zeta
assign ( segid $segid and resid $resid and name C3' )
( segid $segid and resid $resid and name O3' )
( segid $segid and resid $rfoll and name P )
( segid $segid and resid $rfoll and name O5' )
1.0 $dihedral_zeta $error_zeta 2
scale 200.0
end
end if
end loop resid
end if
else
evaluate ($done=true)
end if
evaluate ($group=$group+1)
end loop bdihe
end if
flags include cdih end
{- C1'-C1' virtual bond length restraints -}
noe
class hres
averaging hres cent
potential hres square
sqconstant hres 1.
sqexponent hres 2
scale hres 70.
end
if (&dna_pick_c1 = true) then
evaluate ($pair=1)
evaluate ($done=false)
while ( $done = false ) loop noe
if ( &exist_base_a_$pair = true ) then
if ( &exist_base_b_$pair = true ) then
show ( resname ) ( &base_a_$pair and name C1' )
evaluate ($ares=$result)
show ( resname ) ( &base_b_$pair and name C1' )
evaluate ($bres=$result)
pick bond
(&base_a_$pair and name C1')
(&base_b_$pair and name C1')
geometry
evaluate ($c1c1=$result)
noe
assign (&base_a_$pair and name C1')
(&base_b_$pair and name C1') $c1c1 &c1_low &c1_up
end
end if
else
evaluate ($done=true)
end if
evaluate ($pair=$pair+1)
end loop noe
else
end if
flags include noe end
{- Watson-Crick base pairing -}
noe
class hres
averaging hres cent
potential hres square
sqconstant hres 1.
sqexponent hres 2
scale hres 70.
end
if (&dna_pick_wc = true) then
evaluate ($pair=1)
evaluate ($done=false)
while ( $done = false ) loop noe
if ( &exist_base_a_$pair = true ) then
if ( &exist_base_b_$pair = true ) then
show ( resname ) ( &base_a_$pair and name C1' )
evaluate ($ares=$result)
show ( resname ) ( &base_b_$pair and name C1' )
evaluate ($bres=$result)
if ( $ares = THY ) then
pick bond
(&base_a_$pair and name o4)
(&base_b_$pair and name n6)
geometry
evaluate ($o4n6=$result)
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name n1)
geometry
evaluate ($n3n1=$result)
pick bond
(&base_a_$pair and name h3)
(&base_b_$pair and name n1)
geometry
evaluate ($h3n1=$result)
pick bond
(&base_a_$pair and name o2)
(&base_b_$pair and name h2)
geometry
evaluate ($o2h2=$result)
pick bond
(&base_a_$pair and name o4)
(&base_b_$pair and name n1)
geometry
evaluate ($o4n1=$result)
pick bond
(&base_a_$pair and name o2)
(&base_b_$pair and name n1)
geometry
evaluate ($o2n1=$result)
elseif ( $ares = URI ) then
pick bond
(&base_a_$pair and name o4)
(&base_b_$pair and name n6)
geometry
evaluate ($o4n6=$result)
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name n1)
geometry
evaluate ($n3n1=$result)
pick bond
(&base_a_$pair and name o4)
(&base_b_$pair and name n1)
geometry
evaluate ($o4n1=$result)
pick bond
(&base_a_$pair and name o2)
(&base_b_$pair and name n6)
geometry
evaluate ($o2n6=$result)
elseif ( $ares = ADE ) then
pick bond
(&base_b_$pair and name o4)
(&base_a_$pair and name n6)
geometry
evaluate ($o4n6=$result)
pick bond
(&base_b_$pair and name n3)
(&base_a_$pair and name n1)
geometry
evaluate ($n3n1=$result)
pick bond
(&base_b_$pair and name h3)
(&base_a_$pair and name n1)
geometry
evaluate ($h3n1=$result)
pick bond
(&base_b_$pair and name o2)
(&base_a_$pair and name h2)
geometry
evaluate ($o2h2=$result)
pick bond
(&base_b_$pair and name o4)
(&base_a_$pair and name n1)
geometry
evaluate ($o4n1=$result)
pick bond
(&base_b_$pair and name o2)
(&base_a_$pair and name n1)
geometry
evaluate ($o2n1=$result)
elseif ( $ares = CYT ) then
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name n1)
geometry
evaluate ($n3n1=$result)
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name h1)
geometry
evaluate ($n3h1=$result)
pick bond
(&base_a_$pair and name n4)
(&base_b_$pair and name o6)
geometry
evaluate ($n4o6=$result)
pick bond
(&base_a_$pair and name o2)
(&base_b_$pair and name n2)
geometry
evaluate ($o2h2=$result)
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name o6)
geometry
evaluate ($n3o6=$result)
pick bond
(&base_a_$pair and name n3)
(&base_b_$pair and name n2)
geometry
evaluate ($n3n2=$result)
elseif ( $ares = GUA ) then
pick bond
(&base_b_$pair and name n3)
(&base_a_$pair and name n1)
geometry
evaluate ($n3n1=$result)
pick bond
(&base_b_$pair and name n3)
(&base_a_$pair and name h1)
geometry
evaluate ($n3h1=$result)
pick bond
(&base_b_$pair and name n4)
(&base_a_$pair and name o6)
geometry
evaluate ($n4o6=$result)
pick bond
(&base_b_$pair and name o2)
(&base_a_$pair and name n2)
geometry
evaluate ($o2n2=$result)
pick bond
(&base_b_$pair and name n3)
(&base_a_$pair and name o6)
geometry
evaluate ($n3o6=$result)
pick bond
(&base_b_$pair and name n3)
(&base_a_$pair and name n2)
geometry
evaluate ($n3n2=$result)
end if
noe
if ( $ares = THY ) then
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n6) $o4n6 &wc_low &wc_up
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) $n3n1 &wc_low &wc_up
assign (&base_a_$pair and name h3)
(&base_b_$pair and name n1) $h3n1 &wc_low &wc_up
assign (&base_a_$pair and name o2)
(&base_b_$pair and name h2) $o2h2 &wc_low &wc_up
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n1) $o4n1 &wc_low &wc_up
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n1) $o2n1 &wc_low &wc_up
elseif ( $ares = URI ) then
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n6) $o4n6 &wc_low_uri &wc_up_uri
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) $n3n1 &wc_low_uri &wc_up_uri
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n1) $o4n1 &wc_low_uri &wc_up_uri
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n6) $o2n6 &wc_low_uri &wc_up_uri
elseif ( $ares = ADE ) then
assign (&base_b_$pair and name o4)
(&base_a_$pair and name n6) $o4n6 &wc_low &wc_up
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n1) $n3n1 &wc_low &wc_up
assign (&base_b_$pair and name h3)
(&base_a_$pair and name n1) $h3n1 &wc_low &wc_up
assign (&base_b_$pair and name o2)
(&base_a_$pair and name h2) $o2h2 &wc_low &wc_up
assign (&base_b_$pair and name o4)
(&base_a_$pair and name n1) $o4n1 &wc_low &wc_up
assign (&base_b_$pair and name o2)
(&base_a_$pair and name n1) $o2n1 &wc_low &wc_up
elseif ( $ares = CYT ) then
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) $n3n1 &wc_low &wc_up
assign (&base_a_$pair and name n3)
(&base_b_$pair and name h1) $n3h1 &wc_low &wc_up
assign (&base_a_$pair and name n4)
(&base_b_$pair and name o6) $n4o6 &wc_low &wc_up
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n2) $o2n2 &wc_low &wc_up
assign (&base_a_$pair and name n3)
(&base_b_$pair and name o6) $n3o6 &wc_low &wc_up
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n2) $n3n2 &wc_low &wc_up
elseif ( $ares = GUA ) then
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n1) $n3n1 &wc_low &wc_up
assign (&base_b_$pair and name n3)
(&base_a_$pair and name h1) $n3h1 &wc_low &wc_up
assign (&base_b_$pair and name n4)
(&base_a_$pair and name o6) $n4o6 &wc_low &wc_up
assign (&base_b_$pair and name o2)
(&base_a_$pair and name n2) $o2n2 &wc_low &wc_up
assign (&base_b_$pair and name n3)
(&base_a_$pair and name o6) $n3o6 &wc_low &wc_up
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n2) $n3n2 &wc_low &wc_up
end if
end
end if
else
evaluate ($done=true)
end if
evaluate ($pair=$pair+1)
end loop noe
else
evaluate ($pair=1)
evaluate ($done=false)
while ( $done = false ) loop noe
if ( &exist_base_a_$pair = true ) then
if ( &exist_base_b_$pair = true ) then
show ( resname ) ( &base_a_$pair and name C1' )
evaluate ($ares=$result)
show ( resname ) ( &base_b_$pair and name C1' )
evaluate ($bres=$result)
noe
if ( $ares = THY ) then
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n6) 2.89 0.2 0.2
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) 2.92 0.2 0.2
assign (&base_a_$pair and name h3)
(&base_b_$pair and name n1) 1.87 0.2 0.2
assign (&base_a_$pair and name o2)
(&base_b_$pair and name h2) 2.94 0.2 0.2
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n1) 3.69 0.2 0.2
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n1) 3.67 0.2 0.2
elseif ( $ares = URI ) then
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n6) 2.95 0.01 0.01
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) 2.82 0.01 0.01
assign (&base_a_$pair and name o4)
(&base_b_$pair and name n1) 3.63 0.01 0.01
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n6) 5.40 0.01 0.01
elseif ( $ares = ADE ) then
assign (&base_b_$pair and name o4)
(&base_a_$pair and name n6) 2.89 0.2 0.2
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n1) 2.92 0.2 0.2
assign (&base_b_$pair and name h3)
(&base_a_$pair and name n1) 1.87 0.2 0.2
assign (&base_b_$pair and name o2)
(&base_a_$pair and name h2) 2.94 0.2 0.2
assign (&base_b_$pair and name o4)
(&base_a_$pair and name n1) 3.69 0.2 0.2
assign (&base_b_$pair and name o2)
(&base_a_$pair and name n1) 3.67 0.2 0.2
elseif ( $ares = CYT ) then
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n1) 2.87 0.2 0.2
assign (&base_a_$pair and name n3)
(&base_b_$pair and name h1) 1.86 0.2 0.2
assign (&base_a_$pair and name n4)
(&base_b_$pair and name o6) 2.81 0.2 0.2
assign (&base_a_$pair and name o2)
(&base_b_$pair and name n2) 2.81 0.2 0.2
assign (&base_a_$pair and name n3)
(&base_b_$pair and name o6) 3.58 0.2 0.2
assign (&base_a_$pair and name n3)
(&base_b_$pair and name n2) 3.63 0.2 0.2
elseif ( $ares = GUA ) then
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n1) 2.87 0.2 0.2
assign (&base_b_$pair and name n3)
(&base_a_$pair and name h1) 1.86 0.2 0.2
assign (&base_b_$pair and name n4)
(&base_a_$pair and name o6) 2.81 0.2 0.2
assign (&base_b_$pair and name o2)
(&base_a_$pair and name n2) 2.81 0.2 0.2
assign (&base_b_$pair and name n3)
(&base_a_$pair and name o6) 3.58 0.2 0.2
assign (&base_b_$pair and name n3)
(&base_a_$pair and name n2) 3.63 0.2 0.2
end if
end
end if
else
evaluate ($done=true)
end if
evaluate ($pair=$pair+1)
end loop noe
end if
flags include noe end
set message=off echo=off end
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